Ancestrally, they claim descent from a group of Israelite inhabitants from the tribes of Joseph and Levi (another Benjamin tribe branch), who have connections to ancient Samaria from the beginning of the Babylonian Exile up to the Samaritan Kingdom of Baba Rabba. The Samaritans, however, derive their name not from this geographical designation, but rather from the Hebrew term Shamerim שַמֶרִים, "Keepers [of the Law]".

In the Talmud, a central post-exilic religious text of Judaism, their claim of ancestral origin is disputed, and in those texts they are called Cutheans (Hebrew: כותים‎, Kuthim), allegedly from the ancient city of Cuthah (Kutha), geographically located in what is today Iraq. Modern genetics has suggested some truth to both the claims of the Samaritans and Jewish accounts in the Talmud.

Although historically they were a large community — up to more than a million in late Roman times, then gradually reduced to several tens of thousands up to a few centuries ago — their unprecedented demographic shrinkage has been a result of various historical events, including most notably the bloody repression of the Third Samaritan Revolt (529 AD) against the Byzantine Christian rulers and the mass conversion to Islam in the Early Muslim period of Palestine. According to their tally, as of November 1, 2007, there were 712 Samaritans living almost exclusively in two localities, one in Kiryat Luza on Mount Gerizim near the city of Nablus in the West Bank, and the other in the Israeli city of Holon. There are, however, followers of various backgrounds adhering to Samaritan traditions outside of Israel especially in the United States.